Has anyone upgraded their RE 3.5" standard lift to the 3.5" super flex? If I look at it correctly, the only thing that is different is the super flex comes with RE Discos and fixed F/R lower control arms. Right?

Anyone done this upgrade? If so, was their a difference noted on and off road?

You don't have to use RE parts to upgrade.
The main reason for upgrading the arms is that they have a flex joint to help with articulation and they are a tad longer than stock to help regain the bit of wheelbase you lost when lifting. The disco's are a great improvement for offroad.
For instance you could get JKS discos and Currie or Rokmen control arms - there's no reason you can't mix and match.
I have Pro Comp 4" springs, JKS dicos and JKS upper control arms. I have RE Superflex lower adjustable control arms and a Terflex adjustable trackbar.
Any control arms you get make sure they have a flex joint and are not just solid arms with bushings.
Jim